metaQuantome tutorial: part I #2039

subinamehta · 2020-09-22T20:59:37Z

This tutorial is for uses who want to create datasets that are compatible with the metaQuantome tool. Second part will follow soon.

topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md

subinamehta · 2020-10-15T14:09:51Z

My gosh..i need a spellcheck

…

On Thu, Oct 15, 2020 at 10:08 AM Saskia Hiltemann ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md <#2039 (comment)> : > + +> ### {% icon hands_on %} Hands-on: Remove # from peptide header +> 1. {% tool [Replace Text](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2) %} with the following parameters: +> - {% icon param-file %} *"File to process"*: `Unipept_Function` (output of **Unipept** {% icon tool %}) +> - In *"Replacement"*: +> - {% icon param-repeat %} *"Insert Replacement"* +> - *"Find pattern"*: `#peptide` +> - *"Replace with:"*: `peptide` +> +> 2. Rename file as All_functions +{: .hands_on} + + +## *Filter* - EC values + +We are using this Query tabular ot rename the output that we obtained from the Cut column tool. ot -> to? And I guess this tool does more than rename output from the cut tool? maybe have a look at this? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2039 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGP3A7OSER4FVLX52S6RARLSK366PANCNFSM4RWHUM6Q> .

-- *Subina Mehta* Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455 Lab: 612-624-0381 Phone: 612-500-8841 Email: *smehta@umn.edu <smehta@umn.edu>* *www.galaxyp.org* <http://www.galaxyp.org>

…al into metaquantome

typo fixed

malloryfreeberg · 2020-10-15T18:29:15Z

I'm following the "Hands-on: Interpretation of Search GUI" step, which instructs to set: "Compress results into a single zip file": Yes:

However, when I run the tool with this parameter, there is only one output produced that is a zipped dataset:

And I can't select any individual reports for the next two "Select" steps. When I check what parameters were used when I ran the workflow, I see that the parameter is set to: "Compress results into a single zip file": No:

Also, in the workflow only 4 reports are selected to be generated instead of all reports (as shown in the tutorial).

Please update this step in the tutorial to be sure that usable datasets are produced. I suspect you can either set "Compress results into a single zip file" and "Also export reports out of the zip" parameters both to Yes or set both to No to make sure the individual reports are generated in the history.

malloryfreeberg · 2020-10-15T18:50:08Z

topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md

+> ### {% icon hands_on %} Hands-on: Search sequence databases
+> 1. {% tool [Search GUI](toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1) %} with the following parameters:
+>    - {% icon param-file %} *"Protein Database"*: `ProteinDB_cRAP.fasta`
+>    - {% icon param-file %} *"Input Peak Lists (mgf)"*: `output` (output of **msconvert** {% icon tool %})


Suggested change

> - {% icon param-file %} *"Input Peak Lists (mgf)"*: `output` (output of **msconvert** {% icon tool %})

> - {% icon param-collection %} *"Input Peak Lists (mgf)"*: `output` (output of **msconvert** {% icon tool %})

topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md

subinamehta · 2020-10-15T19:21:14Z

I dont think that should be right..the input is mzml..if that is then it is a problem

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On Thu, Oct 15, 2020 at 3:16 PM Mallory Freeberg ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md <#2039 (comment)> : > +> +{: .question} + + +## *Removing file extensions for Quantification* +This is a data manipulation step to make the data compatible with other downstream processing tools. The Replace text tool replaces the .mgf extension from the PSM report so that it can be used as an input for FlashLFQ. +> +> ### {% icon hands_on %} Hands-on: Removing file extensions +> +> +> 1. {% tool [Replace Text](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3) %} with the following parameters: +> - {% icon param-file %} *"File to process"*: `PSM_Report_no_contaminants` (output of **Select** {% icon tool %}) +> - In *"Replacement"*: +> - {% icon param-repeat %} *"Insert Replacement"* +> - *"in column"*: `c10` +> - *"Find pattern"*: `.mzml.mgf` ⬇️ Suggested change -> - *"Find pattern"*: `.mzml.mgf` +> - *"Find pattern"*: `.raw.mgf` — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2039 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGP3A7PUQBVBUPGDPPJZLPLSK5DB7ANCNFSM4RWHUM6Q> .

-- *Subina Mehta* Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455 Lab: 612-624-0381 Phone: 612-500-8841 Email: *smehta@umn.edu <smehta@umn.edu>* *www.galaxyp.org* <http://www.galaxyp.org>

topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md

malloryfreeberg · 2020-10-15T19:24:29Z

I dont think that should be right..the input is mzml..if that is then it is a problem

Weird. This is what I see when I look at my history from running the workflow (which was successful):

subinamehta · 2020-10-15T19:33:01Z

I dont think that should be right..the input is mzml..if that is then it is a problem

Weird. This is what I see when I look at my history from running the workflow (which was successful):

Yeah..it ran but FlashLFQ might have given empty output...
I made changes to the workflow..It was a WIP when the tutorial was created..so I think I didnt realize that there was an error in the replace expression..Thankyou for catching this.

malloryfreeberg · 2020-10-15T19:35:09Z

Yeah..it ran but FlashLFQ might have given empty output...
I made changes to the workflow..It was a WIP when the tutorial was created..so I think I didnt realize that there was an error in the replace expression..Thankyou for catching this.

Thanks for the explanation. I'll re-run the updated workflow and continue working through the tutorial step-by-step as well.

topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md

malloryfreeberg · 2020-10-15T22:03:56Z

Hi @subinamehta

The tutorial is great! 🎉 🎉 🎉 It's clear a lot of work went into creating it, so kudos to you and all the other contributors for a job well done.

The last thing to look at is the newest version of the workflow. After running it, a few of the datasets are empty: items 27, 30, and 34 in this history.

Just want to check whether this was expected, or if the workflow needs adjusted. I think this is the last change before merging!

subinamehta · 2020-10-15T23:09:05Z

Done! In the workflow, it was written.mzML rather than .mzml..so the regex never happened... I reran the tools with the changes and it worked..I fixed the workflow also... https://usegalaxy.eu/u/subina/h/imported-metaquantome-data-creation-tutorial-workflow---v2

…

On Thu, Oct 15, 2020 at 6:04 PM Mallory Freeberg ***@***.***> wrote: Hi @subinamehta <https://github.com/subinamehta> The tutorial is great! 🎉 🎉 🎉 It's clear a lot of work went into creating it, so kudos to you and all the other contributors for a job well done. The last thing to look at is the newest version of the workflow. After running it, a few of the datasets are empty: items 27, 30, and 34 in this history <https://usegalaxy.eu/u/ef57a2de41414feea0dc0ddfedf02a9d/h/metaquantome-data-creation-tutorial-workflow-v2> . Just want to check whether this was expected, or if the workflow needs adjusted. I think this is the last change before merging! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2039 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGP3A7O2AURHHVV7TZXBCGDSK5WVVANCNFSM4RWHUM6Q> .

-- *Subina Mehta* Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455 Lab: 612-624-0381 Phone: 612-500-8841 Email: *smehta@umn.edu <smehta@umn.edu>* *www.galaxyp.org* <http://www.galaxyp.org>

malloryfreeberg

LGTM!

Great job @subinamehta ! 🎉

Happy for you to merge now, @shiltemann 👍

shiltemann · 2020-10-16T12:55:45Z

awesome, thanks @subinamehta and team! And thanks @malloryfreeberg for the great review! 🎉

subinamehta · 2020-10-16T13:29:03Z

Thanks to you both Saskia and Mallory for your help on making this possible!!! Time to work on the next one!

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On Fri, Oct 16, 2020 at 8:56 AM Saskia Hiltemann ***@***.***> wrote: awesome, thanks @subinamehta <https://github.com/subinamehta> and team! And thanks @malloryfreeberg <https://github.com/malloryfreeberg> for the great review! 🎉 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2039 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGP3A7JQNSQB2FJNVUKPL4DSLA7GHANCNFSM4RWHUM6Q> .

-- *Subina Mehta* Bioinformatics Researcher Dept. of Biochemistry, Molecular Biology and Biophysics University of Minnesota 7-166 MCB 420 Washington Ave SE Minneapolis, MN 55455 Lab: 612-624-0381 Phone: 612-500-8841 Email: *smehta@umn.edu <smehta@umn.edu>* *www.galaxyp.org* <http://www.galaxyp.org>

shiltemann and others added 30 commits September 17, 2020 17:49

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shiltemann reviewed Oct 15, 2020

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